The prototypical harem story features a number of characters, usually with an everyman-type one boy as the lead along with three or more girls whose personalities are often stock characters popular in moe fandom. Occasionally this situation simply exists due to the gender bias and fanservice focus of bishoujo anime, where female characters often greatly outnumber males for marketing purposes.
Many are based on or evocative of renai games, wherein the player generally picks one girl to pursue and follow an established storyline (i.e., 'path') with her. Later adaptations with linear stories, wishing to avoid alienating fans of particular girls by only following one path, may keep all the girls on the same level of "importance" romantically with the lead -- thus creating the illusion of a harem. Because of this, the term does not necessarily imply sexual connotations. Most members of the "harem" often have some other emotional attachment to the lead such as a longtime friendship, rivalry, perception of the lead as a role model, or as a family surrogate.
Some series, such as Ai Yori Aoshi, are designed such that the main character focuses only on one of the girls immediately, with the audience being implicitly aware it is the canonical choice. Other females merely exist to provide temptations, subplots, humorous obstacles, or just cause general chaos. In particular, the second most popular female character in a series is often an inversion of the main girl's personality, providing an outlet for fans who do not like the main girl (e.g., the tomboyish Tina in Ai Yori Aoshi, the series' second most popular character, is a near inversion of main girl Aoi's Yamato Nadeshiko tone.) Others follow their visual novel and renai game roots more closely, such as the adaptations of Shuffle! which remain unspecific as to which girl the main character is most interested in until near the end.
Harem anime often suffer from ending without the romance actually being resolved. This is usually a production issue caused by adaptations begun and completed before the original version has actually ended. For example, Strawberry 100% manga ends with its male protagonist being in a relationship with one of the girls, while in the anime—which finished a few months before the manga—he does not. A common in-plot explanation to this problem is the implication the protagonist remains to be single in order not to alienate any of the female character's feelings, especially if he sees them over time as an extension of his family. Another common theme associated with the protagonist is the obligation to give up one's own happiness to preserve that of another, even if those efforts aren't overtly or immediately rewarded.
Harem titles have experienced a backlash from some anime fans, particularly from females, due to recurring usage of fan service in series with the genre designation.
Action-based stories have occasionally incorporated harem themes - often with a sense of humorous self-awareness - where the girls have a particular ability to help the protagonist in a journey or in fights (e.g., Tenchi Muyo!, Rosario + Vampire, and Negima!: Magister Negi Magi).